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Is There an Optimal Substitution Matrix for Contact Prediction with Correlated Mutations?
July/August 2011 (vol. 8 no. 4)
pp. 1017-1028
ASCII Text
x 
 
Pietro Di Lena, Piero Fariselli, Luciano Margara, Marco Vassura, Rita Casadio, "Is There an Optimal Substitution Matrix for Contact Prediction with Correlated Mutations?," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. 4, pp. 1017-1028, July/August, 2011.
 
 
BibTex
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@article{ 10.1109/TCBB.2010.91,
author = {Pietro Di Lena and Piero Fariselli and Luciano Margara and Marco Vassura and Rita Casadio},
title = {Is There an Optimal Substitution Matrix for Contact Prediction with Correlated Mutations?},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {8},
number = {4},
issn = {1545-5963},
year = {2011},
pages = {1017-1028},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.91},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
TI - Is There an Optimal Substitution Matrix for Contact Prediction with Correlated Mutations?
IS - 4
SN - 1545-5963
SP1017
EP1028
EPD - 1017-1028
A1 - Pietro Di Lena,
A1 - Piero Fariselli,
A1 - Luciano Margara,
A1 - Marco Vassura,
A1 - Rita Casadio,
PY - 2011
KW - Protein contact prediction
KW - correlated mutations
KW - similarity matrix.
VL - 8
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 
Pietro Di Lena, University of Bologna, Bologna
Piero Fariselli, University of Bologna, Bologna
Luciano Margara, University of Bologna, Bologna
Marco Vassura, University of Bologna, Bologna
Rita Casadio, University of Bologna, Bologna
Correlated mutations in proteins are believed to occur in order to preserve the protein functional folding through evolution. Their values can be deduced from sequence and/or structural alignments and are indicative of residue contacts in the protein three-dimensional structure. A correlation among pairs of residues is routinely evaluated with the Pearson correlation coefficient and the MCLACHLAN similarity matrix. In literature, there is no justification for the adoption of the MCLACHLAN instead of other substitution matrices. In this paper, we approach the problem of computing the optimal similarity matrix for contact prediction with correlated mutations, i.e., the similarity matrix that maximizes the accuracy of contact prediction with correlated mutations. We describe an optimization procedure, based on the gradient descent method, for computing the optimal similarity matrix and perform an extensive number of experimental tests. Our tests show that there is a large number of optimal matrices that perform similarly to MCLACHLAN. We also obtain that the upper limit to the accuracy achievable in protein contact prediction is independent of the optimized similarity matrix. This suggests that the poor scoring of the correlated mutations approach may be due to the choice of the linear correlation function in evaluating correlated mutations.

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Index Terms:
Protein contact prediction, correlated mutations, similarity matrix.
Citation:
Pietro Di Lena, Piero Fariselli, Luciano Margara, Marco Vassura, Rita Casadio, "Is There an Optimal Substitution Matrix for Contact Prediction with Correlated Mutations?," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. 4, pp. 1017-1028, July-Aug. 2011, doi:10.1109/TCBB.2010.91
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